Annotations and databases

After extensive analysis of the protein spots has been carried out either by Melanie 3 or through external programs, including protein identification as detailed in Section 4.4, the 2-DE images may be annotated. Melanie 3 provides comprehensive annotation capabilities in order to include into the gel image all related data and information that has been acquired. Each point and each spot in a 2-DE image may given an annotation. Annotations can be added either manually, or they may be imported from an external database, for example through a Laboratory Information Management System (LIMS). Any kind of annotations may be attached to a spot or pixel, as for example the protein ID, a SWISS-2DPAGE ID, a landmark, calibration values (pI, Mr, intensities) or comments, as well as links to external files such as text files or MS spectra and also Internet links. Figure 4.6 shows a zoomed-in portion of an E. coli 2-DE gel, a spot corresponding to Elongation factor TU (EFTU_ECOLI) being selected and highlighted in green. An annotation with seven fields (labels) is attached to it. By double clicking on the various labels, the corresponding piece of information is displayed. In the case of the Accession number (P02990), it launches the default Web browser and requests the corresponding database entry from the user-defined database (here SWISS-2DPAGE on the ExPASy Web server). The database may be on the Web or it can be local. The label «» links to the corresponding URL. A double-click on "AAComposition" opens an Excel file containing the amino acid composition of the protein. "Peptide Masses" displays the list of peptide masses obtained from an MS spectrum, while "MS Spectrum" launches an external program that displays the original spectrum.

10) Mr describes the apparent molecular mass of a protein. That means the position on a calibrated molecular weight scale where the protein of interest is migrating. Mw means molecular weight, in a general manner.

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The annotations in Melanie are of various formats and can include active links to various types of information, such as hyperlinks to database entries, to spectra, to textual information, to tables, etc.

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Annotations may also be exported to external, non-proprietary databases. For example, one can export the accession numbers of all identified proteins and automatically upgrade the SWISS-2DPAGE database.

Continue reading here: Data analysis

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